Every since updating to 1.9 we have had overworld mobs spawning in the Nether, even though this world is not generated by TC, only the overworld is. The overworld and nether are both default worlds, we don't use multiverse for these.

I'm fairly certain this issue is caused by TC as I found this spigot thread which describes the same issue I'm having (which was solved when they removed TC).

Can confirm. I just had to disable TerrainControl to get zombie pigmen and ghasts spawning in the nether again.
I only use TerrainControl for my main overworld.

I also found the cause of the issue to be TerrainControl after looking at this forum post: https://www.spigotmc.org/threads/nether-spawning-wrong-mobs.139295/

I haven't seen this on my server, which is a survival server with TerrainControl only on the main world. So I guess this only happens if the main world doesn't use TC, but another world does?

Our main (default) world does use TC though.